An Interactive Gene Ontology Browser for Proteomics Projects

GOTreePlus User Manual

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1.What is GOTreePlus?
GOTreePlus is an interactive Gene Ontology Browser to allow biologists to easily identify GO terms of importance while visualizing them in the gene ontology structure. It was built using the TreePlus control developed at the University of Maryland's Human-Computer Interaction Lab and the Pie Chart control developed at Microsoft Research.

GOTreePlus consists of two lists (GO term list and gene list) on the left and TreePlus on the right

2.Download and Installation
GOTreePlus is freely downloadable for non-commercial use (academic and/or research purposes) from the download page.
3.Open Files
Select "Open Files..." menu item from the "File" menu.
file open menu

Select the source file and annotation file using "Open..." buttons in the "OpenFiles" dialog.
file open dialog

"Mapping field" is the field in the annotation file to which the first column in the source file is mapped.
There are two fields that can be used as a mapping field: 1) DB_Object_ID (e.g. UniProt ID) and 2) DB_Object_Symbol (e.g. UniProt Symbol).
Default mapping filed is DB_Object_Symbol.
3.Input File Format
GOTreePlus reads 2 user input files; 1 source file and 1 annotation file. Both files are tab-delimited text files.
GO Annotation files are available at the Gene Ontology website.

Source File Format
  • First two lines will be ignored. The first line can be a description of the dataset. The second line has column headers.
  • As shown below, the first column should be an id, the second should be a value, and the third should be a name.
        input soruce file
        Download this sample input file

Annotation File Format
Gene Ontology annotation files are tab-delimited text files, which follows the GO annotation file format guide.
  • Any line starts with '!' will be ignored.
  • As shown below, the second column should be "DB_Object_ID" (e.g. UniProt ID) and the third column should be "DB_Object_Symbol" (e.g. UnitProt Symbol).
  • The ninth column should be the character code to represent a name space; 'C' for Cellular Component, 'F' for Molecular Function, and 'P' for Biological Process.
        annotation file
        Download this annotation file for the sample input file
        or go to GO Annotations page and select the annotation file for "Homo sapiens."
4.Search for GO Terms and Proteins/Genes
 GOTreePlus provides a way to search for specific GO terms – a simple substring match either by name (e.g., "reproduction") or by id (e.g., "GO:0007242"). Search results are shown in the GO terms list. When users select a GO term from the list, the selected term is shown in the gene ontology structure in TreePlus. If the "GO Terms" radio button is selected, the protens/genes list is updated with the items associated with the selected GO term. The number of proteins/genes in the proteins/genes list is also updated and shown by the "Proteins/Genes" radio button.

Similarly, users can also search proteins/genes by id or name (e.g., "placental growth factor") given in the input source file. Labels in the proteins/genes list are grayed out if there is no GO term associated with the item in the current name space. When users select an item from the proteins/genes list, all GO terms related to the selected item are shown in the gene ontology structure in TreePlus. If the "Proteins/Genes" radio button is selected, the GO term list is updated with the GO terms associated with the selected proteins/genes. The number of GO terms in the list is also updated and shown by the "GO Terms" radio button.

5.TreePlus Control
  TreePlus was originally developed in the Human-Computer Interaction Lab at the University of Maryland. It is an interactive graph visualization system based on a tree-style layout. In GOTreePlus, the TreePlus control transforms the Gene Ontology structure (a directed acyclic graph) into a tree. It distinguishes the two relationships (is-a and part-of) in GO by using different type of links. Each node in the TreePlus control has six attributes: name, id, the number of its own annotations, sum of its descendantsí and its own annotations, average value of the proteins mapped to this node, and average value of the proteins mapped to this or its descendants. Each GO node in the TreePlus control has a colored dot that shows up or down regulation of the proteins/gens mapped to the node. As shown in the legend, orange color indicates up-regulation and purple color indicates down-regulation.
GO node

Name Space
Since three name spaces "Biological Process, Cellular Component, and Molecular Function" are disjoint from each other, GOTreePlus visualizes one name space at a time. Users can select one name space among the three using the combo box above the GO term list. The search for GO terms is performed within the selected name space.
name space

Categorize by
Users can choose either "Own Annotation" (average value of the proteins mapped to a node) or "Total Annotation" (average value of the proteins mapped to a node or its descendants) to color the circular dot in GO nodes.

Count Only
When users want to see how only "up-regulated" proteins are mapped to GO, users can select "Up" in this combobox. When they are interested in only the "down-regulated" proteins, they can choose "Down" in the combobox. "All" is the default value with which GOTreePlus uses all proteins regardless of up/down regulation.

Order By
Users can order child nodes of a GO node according to "Own Annotation" (number of its own annotation) or "Total Annotation" (sum of its descendants' and its own annotation).

Users can reset the TreeControl to the initial view where the top-level node of the current ontology is open.

Hide Legend
Users can hide the legend to see only the GO structure in the TreePlus control.

Fit in Window
The TreePlus control scales the current GO display to show all open nodes within the GOTreePlus control.

Default Size
This resets the zoom-level to the initial level.

Users can zoom in or out by dragging the slider bar. Users can pan the GO structure display as well by dragging the canvas.

7.Save as Image
 GOTreePlus allows users to save the current gene ontology structure as an image file. It supports 5 image file formats; PNG, JPG, BMP, GIF, and TIF.
save as image
8.Pop-up Menu
 Users can right-click on any GO node at the TreePlus control to show a pop-up menu.

pop-up menu

  • Set as Root
    Unlike other GO browsers, GOTreePlus enables users to select any GO term and make it the root node to initiate a focused exploration from the node.
    set a root:before
    set a root:after

  • Retrieve annotated proteins/genes
    Users can also populate the proteins/genes list with the proteins/genes mapped to the selected GO node.
  • Export annotated proteins/genes (only this node)
    Users can save the proteins/genes mapped to the selected node in a text file.
  • Export annotated proteins/genes (this node & below)
    Users can save the proteins/genes mapped to the selected node or its descendants in a text file.
  • Show annotation distribution
    Users can select any node to see a localized overview of annotation distribution over its children nodes in a standard pie chart with a coordinated list view.
    pie chart
    The pie chart is coordinated with the list control below and the TreePlus control. When users mouse over on a slice at the pie chart, the corresponding item on the list and the corresponding node on the TreePlus control will be highlighted. When users select an item on the list control, the corresponding parts in the pie chart and the TreePlus control are highlighted.

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